Methods and Kits for the Rapid Determination of Patients at High Risk of Death During Septic Shock

Abstract

The present invention relates to the field of treatment of serious medical syndromes such as severe sepsis and septic shock. In particular, the present invention provides methods and kits to obtain an early evaluation of mortality risk and help therapeutic decisions for patients in severe sepsis with two organ failures, for example for patients in septic shock with one additional organ failure. The methods of the invention are based on the analysis of an expression profile of one or several genes selected in the group consisting of HLA-DRB4, FOSB, GPR109B, RBP7, TLR7, IL15, HLA-C, AMFR, LOC96610, IRF5, MGC29506, EDG3, IGLV1-44, IFIT2, IFI44, EPSTI1, TNFRSF17, AREG, THBS1, CTLS1, TFPI, PHACTR2, PFKFB2 and CHIT1.

1 . Use of at least one gene selected in the group consisting of HLA-DRB4, FOSB, GPR109B, RBP7, TLR7, IL15, HLA-C, AMFR, LOC96610, IRF5, MGC29506, EDG3, IGLV1-44, IFIT2, IFI44, EPSTI1, TNFRSF17, AREG, THBS1, CTLS1, TFPI, PHACTR2, PFKFB2 and CHIT1, as a prognosis marker for a patient in severe sepsis with at least two organ failures. 
     
     
         2 . The use of  claim 1 , wherein said at least one gene is selected in the group consisting of HLA-DRB4, AREG, FOSB, GPR109B, RBP7, TLR7, THBS1 and CTLS1. 
     
     
         3 . The use of  claim 1 , wherein said at least one gene is selected in the group consisting of HLA-DRB4, AREG and FOSB. 
     
     
         4 . A method for in vitro establishing a prognosis for a subject in severe sepsis with at least two organ failures, comprising the following steps:
 (i) from a sample from said subject, obtaining an expression profile of a set of genes comprising at least two genes selected in the group consisting of HLA-DRB4, FOSB, GPR109B, RBP7, TLR7, IL15, HLA-C, AMFR, LOC96610, IRF5, MGC29506, EDG3, IGLV1-44, IFIT2, IFI44, EPSTI1, TNFRSF17, AREG, THBS1, CTLS1, TFPI, PHACTR2, PFKFB2 and CHIT1; and   (ii) comparing said obtained expression profile to one or two reference expression profiles to establish a prognosis for said subject.   
     
     
         5 . The method according to  claim 4 , comprising the following steps:
 (i) the expression levels of n (n≧2) genes are measured in a biological sample from said patient, wherein at least two of these genes are selected from the group consisting of HLA-DRB4, FOSB, GPR109B, RBP7, TLR7, IL15, HLA-C, AMFR, LOC96610, IRF5, MGC29506, EDG3, IGLV1-44, IFIT2, IFI44, EPSTI1, TNFRSF17, AREG, THBS1, CTLS1, TFPI, PHACTR2, PFKFB2 and CHIT1;   (ii) a score is calculated as follows:   
       
         
           
             
               
                 
                   
                     Score 
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                         y 
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                           ∑ 
                           
                             j 
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                           n 
                         
                          
                         
                           
                             
                               β 
                               ^ 
                             
                             j 
                           
                            
                           
                             
                               X 
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                             j 
                           
                         
                       
                     
                   
                 
                 
                   
                     ( 
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         wherein {tilde over (X)} j  (j=1 to n) are the expression levels of said genes measured in said biological sample, and {circumflex over (β)} j  (j=1 to n) are calculated regression coefficients; 
         (iii) the score obtained in step (ii) is interpreted by comparing it to a predetermined threshold. 
       
     
     
         6 . The method according to  claim 4 , wherein at least one of the genes selected in step (i) is selected in the group consisting of HLA-DRB4, AREG and FOSB. 
     
     
         7 . The method according to  claim 4 , wherein the set of genes selected in step (i) comprises HLA-DRB4, AREG and FOSB. 
     
     
         8 . The method according to  claim 4 , wherein the set of genes selected in step (i) comprises HLA-DRB4, AREG, FOSB, GPR109B, RBP7, TLR7, THBS1 and CTLS1. 
     
     
         9 . The method according to  claim 4 , wherein the set of genes selected in step (i) comprises HLA-DRB4, FOSB, GPR109B, RBP7, TLR7, IL15, HLA-C, AMFR, LOC96610, IRF5, MGC29506, EDG3, IGLV1-44, IFIT2, EPSTI1, TNFRSF17, AREG, THBS1, CTLS1, TFPI, PHACTR2, PFKFB2 and CHIT1. 
     
     
         10 . The method according to  claim 4 , for establishing a prognosis for a patient in septic shock with at least one additional organ failure. 
     
     
         11 . The method according to  claim 4 , wherein said biological sample is (i) a whole blood sample or (ii) a blood fraction comprising or consisting of peripheral blood mononuclear cells, or (iii) a blood fraction comprising or consisting of white blood cells after removal of mature granulocytes. 
     
     
         12 . A method for determining if a subject in severe sepsis with at least two organ failures can benefit from the administration of a medicinal product, comprising a step of in vitro determining if said patient expresses HLA-DRB4. 
     
     
         13 . The method according to  claim 12 , wherein the absence of HLA-DRB4 expression indicates that administration of Activated Protein C to said patient is appropriate. 
     
     
         14 . The method of  claim 12 , wherein in the absence of HLA-DRB4 expression, up-regulation of one or several genes selected amongst FOSB, GPR109B, RBP7, TLR7, IL15, HLA-C, AMFR, LOC96610, IRF5, MGC29506, EDG3, IGLV1-44, IFIT2, IFI44, EPSTI1 and TNFRSF17, and/or down-regulation of one or several genes selected amongst AREG, THBS1, CTLS1, TFPI, PHACTR2, PFKFB2 and CHIT1 indicate(s) that said patient will be a good responder to Activated Protein C. 
     
     
         15 . A method for in vitro evaluating the efficiency of a pharmaceutical treatment administered to a subject in severe sepsis with at least two organ failures, comprising the following steps:
 (i) from a sample from said subject obtained before the beginning of said pharmaceutical treatment, determining an expression profile of a set of genes comprising at least two genes selected from the group consisting of HLA-DRB4, FOSB, GPR109B, RBP7, TLR7, IL15, HLA-C, AMFR, LOC96610, IRF5, MGC29506, EDG3, IGLV1-44, IFIT2, IFI44, EPSTI1, TNFRSF17, AREG, THBS1, CTLS1, TFPI, PHACTR2, PFKFB2 and CHIT1;   (ii) from at least another sample from said subject, obtained after the beginning of said pharmaceutical treatment, determining an expression profile of the same set of genes as in (i);   (iii) comparing said obtained expression profiles.   
     
     
         16 . The method according to  claim 15 , wherein up-regulation of one or several genes selected amongst FOSB, GPR109B, RBP7, TLR7, IL15, HLA-C, AMFR, LOC96610, IRF5, MGC29506, EDG3, IGLV1-44, IFIT2, IFI44, EPSTI1 and TNFRSF17, and/or down-regulation of one or several genes selected amongst AREG, THBS1, CTLS1, TFPI, PHACTR2, PFKFB2 and CHIT1 following the beginning of the pharmaceutical treatment indicate(s) that said treatment has been beneficial to the patient. 
     
     
         17 . A method for selecting subjects to be enrolled in a clinical trial for evaluating a medicinal product in the treatment of severe sepsis with at least two organ failures, comprising a step of in vitro establishing a prognosis for said subjects, by a method according to  claim 4 . 
     
     
         18 . The method of  claim 17 , wherein the subjects enrolled in the clinical trial are those who have a poor prognosis. 
     
     
         19 . A kit for performing the method according to  claim 4 , comprising one or several pairs of primers, wherein each pair of primers is specific for a gene selected amongst HLA-DRB4, AREG and FOSB. 
     
     
         20 . The kit of  claim 19 , further comprising one or several additional pairs of primers, wherein each pair of primers is specific for one sequence selected from the group consisting of 18S rRNA, GPR109B, RBP7, TLR7, IL15, HLA-C, AMFR, LOC96610, IRF5, MGC29506, EDG3, IGLV1-44, IFIT2, IFI44, EPSTI1, TNFRSF17, THBS1, CTLS1, TFPI, PHACTR2, PFKFB2 and CHIT1 genes. 
     
     
         21 . The kit of  claim 19 , which further comprises reagents and/or enzymes for performing amplification reactions. 
     
     
         22 . A kit for performing the method according to  claim 4 , comprising a chip enabling hybridization of nucleic acids specific for at least two genes selected in the group consisting of HLA-DRB4, AREG, FOSB, GPR109B, RBP7, TLR7, IL15, HLA-C, AMFR, LOC96610, IRF5, MGC29506, EDG3, IGLV1-44, IFIT2, IFI44, EPSTI1, TNFRSF17, THBS1, CTLS1, TFPI, PHACTR2, PFKFB2 and CHIT1. 
     
     
         23 . The kit of any of  claim 22 , which further comprises reagents for PBMC isolation.